From: Bassam Haddad (
Date: Tue Jun 02 2020 - 12:33:03 CDT

Hi Yogesh,

You are welcome to any of the scripts you find from my lab's Github
<> page, and feel free to contact
me personally if you have questions regarding them. These two scripts aught
to help you:

HOLE-APBS_gen.tcl will create inputs for you for HOLE and APBS (you can
comment these out) from every frame that you have loaded into memory. Then
you can use to run Hole on all of your frames. From here
you'll just have to parse the data – there is an `awk` line in the script
that you can modify to retrieve whatever information you want.


On Tue, Jun 2, 2020 at 10:08 AM Yogesh Sharma <>

> Thank you sir,
> Sounds reasonable but I am new to md simulation s. I have used hole
> program for average pore diameter analysis over the trajectory. But I m
> not skilled enough to dig deep into codes. Do you have some script that you
> might have used earlier?
> On Tuesday, June 2, 2020, Bassam Haddad <> wrote:
>> Hi Yogesh,
>> You can use Hole <> to calculate the minimum
>> pore radii at each z-height, this will tell you where the constriction is,
>> and which amino acid is contributing to the minimum radii. You'll just have
>> to parse the hole outputs.
>> Best of luck,
>> Bassam
>> On Tue, Jun 2, 2020 at 4:41 AM Yogesh Sharma <>
>> wrote:
>>> greetings everyone,
>>> hope you guys are doing good.
>>> I am interested in finding amino acids that are forming constrictions in
>>> protein pore throughout trajectory. I can do it manually for asingle frame
>>> but i am more interested in variations throughout trajectory in that
>>> region. can someone suggest the way ?
>>> *with regards*
>>> *Yogesh Sharma*
> --
> * with regards*
> *Yogesh Sharma*